Mercurial > repos > artbio > gsc_high_dimensions_visualisation

annotate high_dim_visu.R @ 5:569334568afa draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
author artbio
date Mon, 02 Sep 2019 04:39:20 -0400
parents 8e17c31c536a
children 19bef589f876
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0
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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1 # load packages that are provided in the conda env
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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2 options( show.error.messages=F,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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3 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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4 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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5 warnings()
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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6 library(optparse)
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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7 library(FactoMineR)
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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8 library(factoextra)
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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9 library(Rtsne)
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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10 library(ggplot2)
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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11 library(ggfortify)
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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12 library(RColorBrewer)
4
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
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13 library(ClusterR)
5
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
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14 library(data.table)
0
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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15
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16 # Arguments
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17 option_list = list(
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18 make_option(
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19 "--data",
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20 default = NA,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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21 type = 'character',
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22 help = "Input file that contains expression value to visualise"
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23 ),
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24 make_option(
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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25 "--sep",
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26 default = '\t',
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27 type = 'character',
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28 help = "File separator [default : '%default' ]"
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29 ),
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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30 make_option(
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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31 "--colnames",
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32 default = TRUE,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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33 type = 'logical',
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34 help = "Consider first line as header ? [default : '%default' ]"
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35 ),
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36 make_option(
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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37 "--out",
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38 default = "res.tab",
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39 type = 'character',
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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40 help = "Output name [default : '%default' ]"
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41 ),
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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42 make_option(
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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43 "--labels",
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44 default = FALSE,
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45 type = 'logical',
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46 help = "add labels in scatter plots [default : '%default' ]"
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47 ),
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48 make_option(
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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49 "--factor",
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50 default = '',
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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51 type = 'character',
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52 help = "A two column table that specifies factor levels for contrasting data [default : '%default' ]"
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53 ),
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54 make_option(
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55 "--visu_choice",
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56 default = 'PCA',
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57 type = 'character',
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58 help = "visualisation method ('PCA', 'tSNE', 'HCPC') [default : '%default' ]"
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59 ),
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60 make_option(
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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61 "--table_coordinates",
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62 default = '',
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63 type = 'character',
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64 help = "Table with plot coordinates [default : '%default' ]"
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65 ),
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66 make_option(
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67 "--Rtsne_seed",
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68 default = 42,
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69 type = 'integer',
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70 help = "Seed value for reproducibility [default : '%default' ]"
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71 ),
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72 make_option(
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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73 "--Rtsne_dims",
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74 default = 2,
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75 type = 'integer',
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76 help = "Output dimensionality [default : '%default' ]"
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77 ),
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78 make_option(
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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79 "--Rtsne_initial_dims",
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80 default = 50,
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81 type = 'integer',
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82 help = "The number of dimensions that should be retained in the initial PCA step [default : '%default' ]"
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83 ),
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84 make_option(
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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85 "--Rtsne_perplexity",
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86 default = 5.0,
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87 type = 'numeric',
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88 help = "perplexity [default : '%default' ]"
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89 ),
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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diff changeset
90 make_option(
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
91 "--Rtsne_theta",
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
92 default = 1.0,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
93 type = 'numeric',
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
94 help = "theta [default : '%default' ]"
4
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
95 ),
0
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
96 make_option(
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
97 "--Rtsne_max_iter",
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
98 default = 1000,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
99 type = 'integer',
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
100 help = "max_iter [default : '%default' ]"
4
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
101 ),
0
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
102 make_option(
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
103 "--Rtsne_pca",
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
104 default = TRUE,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
105 type = 'logical',
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
106 help = "Whether an initial PCA step should be performed [default : '%default' ]"
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
107 ),
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
108 make_option(
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
109 "--Rtsne_pca_center",
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
110 default = TRUE,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
111 type = 'logical',
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
112 help = "Should data be centered before pca is applied? [default : '%default' ]"
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
113 ),
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
114 make_option(
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
115 "--Rtsne_pca_scale",
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
116 default = FALSE,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
117 type = 'logical',
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
118 help = "Should data be scaled before pca is applied? [default : '%default' ]"
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
119 ),
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
120 make_option(
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
121 "--Rtsne_normalize",
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
122 default = TRUE,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
123 type = 'logical',
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
124 help = "Should data be normalized internally prior to distance calculations? [default : '%default' ]"
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
125 ),
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
126 make_option(
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
127 "--Rtsne_exaggeration_factor",
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
128 default = 12.0,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
129 type = 'numeric',
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
130 help = " Exaggeration factor used to multiply the P matrix in the first part of the optimization [default : '%default' ]"
4
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
131 ),
0
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
132 make_option(
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
133 "--PCA_npc",
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
134 default = 5,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
135 type = 'integer',
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
136 help = "number of dimensions kept in the results [default : '%default' ]"
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
137 ),
4
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
138 make_option(
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
139 "--PCA_x_axis",
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
140 default = 1,
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
141 type = 'integer',
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
142 help = "PC to plot in the x axis [default : '%default' ]"
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
143 ),
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
144 make_option(
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
145 "--PCA_y_axis",
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
146 default = 2,
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
147 type = 'integer',
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
148 help = "PC to plot in the y axis [default : '%default' ]"
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
149 ),
0
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
150 make_option(
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
151 "--HCPC_ncluster",
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
152 default = -1,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
153 type = 'numeric',
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
154 help = "nb.clust, number of clusters to consider in the hierarchical clustering. [default : -1 let HCPC to optimize the number]"
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
155 ),
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
156 make_option(
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
157 "--HCPC_npc",
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
158 default = 5,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
159 type = 'integer',
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
160 help = "npc, number of dimensions which are kept for HCPC analysis [default : '%default' ]"
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
161 ),
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
162 make_option(
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
163 "--HCPC_metric",
5
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
164 default = 'euclidean',
0
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
165 type = 'character',
5
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
166 help = "Metric to be used for calculating dissimilarities between observations, available 'euclidean' or 'manhattan' [default : '%default' ]"
0
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
167 ),
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
168 make_option(
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
169 "--HCPC_method",
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
170 default = 'ward',
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
171 type = 'character',
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
172 help = "Clustering method between 'ward','average','single', 'complete', 'weighted' [default :'%default']"
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
173 ),
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
174 make_option(
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
175 "--pdf_out",
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
176 default = "out.pdf",
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
177 type = 'character',
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
178 help = "pdf of plots [default : '%default' ]"
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
179 ),
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
180 make_option(
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
181 "--HCPC_consol",
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
182 default = 'TRUE',
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
183 type = 'logical',
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
184 help = "If TRUE, a k-means consolidation is performed [default :'%default']"
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
185 ),
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
186 make_option(
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
187 "--HCPC_itermax",
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
188 default = '10',
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
189 type = 'integer',
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
190 help = "The maximum number of iterations for the consolidation [default :'%default']"
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
191 ),
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
192 make_option(
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
193 "--HCPC_min",
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
194 default = '3',
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
195 type = 'integer',
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
196 help = "The least possible number of clusters suggested [default :'%default']"
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
197 ),
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
198 make_option(
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
199 "--HCPC_max",
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
200 default = -1,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
201 type = 'integer',
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
202 help = "The higher possible number of clusters suggested [default :'%default']"
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
203 ),
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
204 make_option(
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
205 "--HCPC_clusterCA",
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
206 default = 'rows',
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
207 type = 'character',
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
208 help = "A string equals to 'rows' or 'columns' for the clustering of Correspondence Analysis results [default :'%default']"
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
209 ),
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
210 make_option(
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
211 "--HCPC_kk",
5
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
212 default = Inf,
0
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
213 type = 'numeric',
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
214 help = "The maximum number of iterations for the consolidation [default :'%default']"
4
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
215 ),
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
216 make_option(
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
217 "--HCPC_clust",
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
218 default = "",
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
219 type = 'character',
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
220 help = "Output result of HCPC clustering : two column table (cell identifiers and clusters) [default :'%default']"
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
221 ),
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
222 make_option(
5
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
223 "--HCPC_mutual_info",
4
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
224 default = "",
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
225 type = "character",
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
226 help = "Output file of external validation of HCPC clustering with factor levels [default :'%default']"
5
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
227 ),
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
228 make_option(
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
229 "--HCPC_cluster_description",
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
230 default = "",
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
231 type = "character",
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
232 help = "Output file with variables most contributing to clustering [default :'%default']"
4
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
233 )
0
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
234 )
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
235
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
236 opt = parse_args(OptionParser(option_list = option_list),
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
237 args = commandArgs(trailingOnly = TRUE))
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
238
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
239 if (opt$sep == "tab") {opt$sep <- "\t"}
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
240 if (opt$sep == "comma") {opt$sep <- ","}
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
241 if(opt$HCPC_max == -1) {opt$HCPC_max <- NULL}
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
242 if(opt$HCPC_kk == -1) {opt$HCPC_kk <- Inf}
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
243
4
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
244 ##Add legend to plot()
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
245 legend.col <- function(col, lev){
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
246
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
247 opar <- par
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
248
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
249 n <- length(col)
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
250
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
251 bx <- par("usr")
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
252
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
253 box.cx <- c(bx[2] + (bx[2] - bx[1]) / 1000,
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
254 bx[2] + (bx[2] - bx[1]) / 1000 + (bx[2] - bx[1]) / 50)
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
255 box.cy <- c(bx[3], bx[3])
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
256 box.sy <- (bx[4] - bx[3]) / n
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
257
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
258 xx <- rep(box.cx, each = 2)
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
259
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
260 par(xpd = TRUE)
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
261 for(i in 1:n){
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
262
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
263 yy <- c(box.cy[1] + (box.sy * (i - 1)),
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
264 box.cy[1] + (box.sy * (i)),
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
265 box.cy[1] + (box.sy * (i)),
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
266 box.cy[1] + (box.sy * (i - 1)))
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
267 polygon(xx, yy, col = col[i], border = col[i])
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
268
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artbio
parents: 3
diff changeset
269 }
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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diff changeset
270 par(new = TRUE)
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artbio
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diff changeset
271 plot(0, 0, type = "n",
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artbio
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diff changeset
272 ylim = c(min(lev), max(lev)),
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artbio
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diff changeset
273 yaxt = "n", ylab = "",
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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diff changeset
274 xaxt = "n", xlab = "",
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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diff changeset
275 frame.plot = FALSE)
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artbio
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diff changeset
276 axis(side = 4, las = 2, tick = FALSE, line = .25)
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artbio
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diff changeset
277 par <- opar
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
278 }
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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diff changeset
279
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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diff changeset
280
0
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
281 data = read.table(
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
282 opt$data,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
283 check.names = FALSE,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
284 header = opt$colnames,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
285 row.names = 1,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
286 sep = opt$sep
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
287 )
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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288
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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289 # Contrasting factor and its colors
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
290 if (opt$factor != '') {
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
291 contrasting_factor <- read.delim(
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
292 opt$factor,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
293 header = TRUE
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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294 )
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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295 rownames(contrasting_factor) <- contrasting_factor[,1]
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
296 contrasting_factor <- contrasting_factor[colnames(data),]
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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297 colnames(contrasting_factor) <- c("id","factor")
4
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artbio
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298 if(is.numeric(contrasting_factor$factor)){
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artbio
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299 factor_cols <- rev(brewer.pal(n = 11, name = "RdYlGn"))[contrasting_factor$factor]
2
7e7a2a4cfce2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit e15ae06208ef1d3d42c0576ed28eb6ba10a36671
artbio
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300 } else {
4
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artbio
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301 contrasting_factor$factor <- as.factor(contrasting_factor$factor)
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artbio
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diff changeset
302 if(nlevels(contrasting_factor$factor) == 2){
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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303 colors_labels <- c("#E41A1C", "#377EB8")
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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diff changeset
304 } else {
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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diff changeset
305 colors_labels <- brewer.pal(nlevels(contrasting_factor$factor), name = 'Paired')
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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diff changeset
306 }
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artbio
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diff changeset
307 factorColors <-
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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diff changeset
308 with(contrasting_factor,
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artbio
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diff changeset
309 data.frame(factor = levels(contrasting_factor$factor),
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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diff changeset
310 color = I(colors_labels)
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artbio
parents: 3
diff changeset
311 )
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
312 )
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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diff changeset
313 factor_cols <- factorColors$color[match(contrasting_factor$factor,
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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diff changeset
314 factorColors$factor)]
2
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artbio
parents: 0
diff changeset
315 }
0
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
316 } else {
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
317 factor_cols <- rep("deepskyblue4", length(rownames(data)))
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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diff changeset
318 }
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
319
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
320 ################ t-SNE ####################
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
321 if (opt$visu_choice == 'tSNE') {
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
322 # filter and transpose df for tsne and pca
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
323 tdf = t(data)
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
324 # make tsne and plot results
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
325 set.seed(opt$Rtsne_seed) ## Sets seed for reproducibility
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
326
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
327 tsne_out <- Rtsne(tdf,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
328 dims = opt$Rtsne_dims,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
329 initial_dims = opt$Rtsne_initial_dims,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
330 perplexity = opt$Rtsne_perplexity ,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
331 theta = opt$Rtsne_theta,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
332 max_iter = opt$Rtsne_max_iter,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
333 pca = opt$Rtsne_pca,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
334 pca_center = opt$Rtsne_pca_center,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
335 pca_scale = opt$Rtsne_pca_scale,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
336 normalize = opt$Rtsne_normalize,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
337 exaggeration_factor=opt$Rtsne_exaggeration_factor)
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
338
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
339 embedding <- as.data.frame(tsne_out$Y[,1:2])
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
340 embedding$Class <- as.factor(rownames(tdf))
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
341 gg_legend = theme(legend.position="right")
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
342 if (opt$factor == '') {
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
343 ggplot(embedding, aes(x=V1, y=V2)) +
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
344 geom_point(size=1, color='deepskyblue4') +
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
345 gg_legend +
4
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artbio
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diff changeset
346 xlab("t-SNE 1") +
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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diff changeset
347 ylab("t-SNE 2") +
0
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
348 ggtitle('t-SNE') +
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
349 if (opt$labels) {
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
350 geom_text(aes(label=Class),hjust=-0.2, vjust=-0.5, size=1.5, color='deepskyblue4')
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
351 }
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
352 } else {
4
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
353 if(is.numeric(contrasting_factor$factor)){
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
354 embedding$factor <- contrasting_factor$factor
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
355 } else {
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
356 embedding$factor <- as.factor(contrasting_factor$factor)
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
357 }
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
358
0
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
359 ggplot(embedding, aes(x=V1, y=V2, color=factor)) +
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
360 geom_point(size=1) + #, color=factor_cols
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
361 gg_legend +
4
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
362 xlab("t-SNE 1") +
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
363 ylab("t-SNE 2") +
0
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
364 ggtitle('t-SNE') +
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
365 if (opt$labels) {
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
366 geom_text(aes(label=Class, colour=factor),hjust=-0.2, vjust=-0.5, size=1.5)
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
367 }
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
368 }
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
369 ggsave(file=opt$pdf_out, device="pdf")
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
370
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
371 #save coordinates table
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
372 if(opt$table_coordinates != ''){
4
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
373 coord_table <- cbind(rownames(tdf), round(as.data.frame(tsne_out$Y), 6))
0
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
374 colnames(coord_table)=c("Cells",paste0("DIM",(1:opt$Rtsne_dims)))
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
375 }
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
376 }
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
377
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
378
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
379 ######### make PCA with FactoMineR #################
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
380 if (opt$visu_choice == 'PCA') {
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
381 pca <- PCA(t(data), ncp=opt$PCA_npc, graph=FALSE)
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
382 pdf(opt$pdf_out)
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
383 if (opt$labels == FALSE) {
4
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
384 plot(pca, axes = c(opt$PCA_x_axis,opt$PCA_y_axis), label="none" , col.ind = factor_cols)
0
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
385 } else {
4
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
386 plot(pca, axes = c(opt$PCA_x_axis,opt$PCA_y_axis), cex=0.2 , col.ind = factor_cols)
0
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
387 }
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
388 if (opt$factor != '') {
4
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
389 if(is.factor(contrasting_factor$factor)) {
0
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
390 legend(x = 'topright',
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
391 legend = as.character(factorColors$factor),
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
392 col = factorColors$color, pch = 16, bty = 'n', xjust = 1, cex=0.7)
4
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
393 } else {
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
394 legend.col(col = rev(brewer.pal(n = 11, name = "RdYlGn")), lev = cut(contrasting_factor$factor, 11, label = FALSE))
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
395 }
0
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
396 }
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
397 dev.off()
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
398
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
399 #save coordinates table
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
400 if(opt$table_coordinates != ''){
4
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
401 coord_table <- cbind(rownames(pca$ind$coord), round(as.data.frame(pca$ind$coord), 6))
0
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
402 colnames(coord_table)=c("Cells",paste0("DIM",(1:opt$PCA_npc)))
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
403 }
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
404
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
405 }
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
406
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
407 ########### make HCPC with FactoMineR ##########
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
408 if (opt$visu_choice == 'HCPC') {
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
409
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
410 # HCPC starts with a PCA
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
411 pca <- PCA(
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
412 t(data),
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
413 ncp = opt$HCPC_npc,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
414 graph = FALSE,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
415 )
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
416
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
417 PCA_IndCoord = as.data.frame(pca$ind$coord) # coordinates of observations in PCA
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
418
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
419 # Hierarchical Clustering On Principal Components Followed By Kmean Clustering
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
420 res.hcpc <- HCPC(pca,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
421 nb.clust=opt$HCPC_ncluster, metric=opt$HCPC_metric, method=opt$HCPC_method,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
422 graph=F,consol=opt$HCPC_consol,iter.max=opt$HCPC_itermax,min=opt$HCPC_min,max=opt$HCPC_max,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
423 cluster.CA=opt$HCPC_clusterCA,kk=opt$HCPC_kk)
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
424 # HCPC plots
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
425 dims <- head(as.data.frame(res.hcpc$call$t$res$eig),2) # dims variances in column 2
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
426 pdf(opt$pdf_out)
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
427 plot(res.hcpc, choice="tree")
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
428 plot(res.hcpc, choice="bar")
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
429 plot(res.hcpc, choice="3D.map")
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
430 if (opt$labels == FALSE) {
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
431 plot(res.hcpc, choice="map", label="none")
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
432 } else {
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
433 plot(res.hcpc, choice="map")
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
434 }
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
435
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
436 # user contrasts on the pca
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
437 if (opt$factor != '') {
4
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
438 plot(pca, label="none", col.ind = factor_cols)
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
439 if(is.factor(contrasting_factor$factor)) {
0
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
440 legend(x = 'topright',
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
441 legend = as.character(factorColors$factor),
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
442 col = factorColors$color, pch = 16, bty = 'n', xjust = 1, cex=0.7)
4
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
443
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
444 ## Normalized Mutual Information
5
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
445 sink(opt$HCPC_mutual_info)
4
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
446 res <- external_validation(
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
447 true_labels = as.numeric(contrasting_factor$factor),
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
448 clusters = as.numeric(res.hcpc$data.clust$clust),
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
449 summary_stats = TRUE
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
450 )
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
451 sink()
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
452
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
453 } else {
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
454 legend.col(col = rev(brewer.pal(n = 11, name = "RdYlGn")), lev = cut(contrasting_factor$factor, 11, label = FALSE))
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
455 }
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
456 }
5
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
457
0
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
458 ## Clusters to which individual observations belong # used ?
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
459 # Clust <- data.frame(Cluster = res.hcpc$data.clust[, (nrow(data) + 1)],
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
460 # Observation = rownames(res.hcpc$data.clust))
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
461 # metadata <- data.frame(Observation=colnames(data), row.names=colnames(data))
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
462 # metadata = merge(y = metadata,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
463 # x = Clust,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
464 # by = "Observation")
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
465
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
466 # unclear utility
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
467 # ObsNumberPerCluster = as.data.frame(table(metadata$Cluster))
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
468 # colnames(ObsNumberPerCluster) = c("Cluster", "ObsNumber")
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
469 #
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
470 # ## Silhouette Plot # not used
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
471 # hc.cut = hcut(PCA_IndCoord,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
472 # k = nlevels(metadata$Cluster),
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
473 # hc_method = "ward.D2")
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
474 #
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
475 # Sil = fviz_silhouette(hc.cut)
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
476 # sil1 = as.data.frame(Sil$data)
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
477
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
478 dev.off()
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
479
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
480 if(opt$table_coordinates != ''){
4
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
481 coord_table <- cbind(Cell=rownames(res.hcpc$call$X),
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
482 round(as.data.frame(res.hcpc$call$X[, -length(res.hcpc$call$X)]), 6),
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
483 as.data.frame(res.hcpc$call$X[, length(res.hcpc$call$X)])
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
484 )
0
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
485 colnames(coord_table)=c("Cells",paste0("DIM",(1:opt$HCPC_npc)),"Cluster")
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
486 }
4
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
487
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
488 if(opt$HCPC_clust != ""){
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
489 res_clustering <- data.frame(Cell = rownames(res.hcpc$data.clust),
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
490 Cluster = res.hcpc$data.clust$clust)
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
491
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
492 }
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
493
5
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
494 # Description of cluster by most contributing variables / gene expressions
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
495
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
496 # first transform list of vectors in a list of dataframes
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
497 extract_description <- lapply(res.hcpc$desc.var$quanti, as.data.frame)
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
498 # second, transfer rownames (genes) to column in the dataframe, before rbinding
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
499 extract_description_w_genes <- Map(cbind,
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
500 extract_description,
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
501 genes= lapply(extract_description, rownames)
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
502 )
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
503 # Then use data.table to collapse all generated dataframe, with the cluster id in first column
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
504 # using the {data.table} rbindlist function
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
505 cluster_description <- rbindlist(extract_description_w_genes, idcol = "cluster_id")
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
506 cluster_description = cluster_description[ ,c(8, 1, 2, 3,4,5,6,7)] # reorganize columns
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
507
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
508
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
509 # Finally, output cluster description data frame
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
510 write.table(
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
511 cluster_description,
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
512 file = opt$HCPC_cluster_description,
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
513 sep = "\t",
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
514 quote = F,
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
515 col.names = T,
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
516 row.names = F
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
517 )
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
518
0
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
519 }
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
520
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
521 ## Return coordinates file to user
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
522
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
523 if(opt$table_coordinates != ''){
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
524 write.table(
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
525 coord_table,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
526 file = opt$table_coordinates,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
527 sep = "\t",
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
528 quote = F,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
529 col.names = T,
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
530 row.names = F
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
531 )
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
532 }
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
533
cad0001b9cfb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff changeset
534
4
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
535 if(opt$HCPC_clust != ""){
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
536 write.table(
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
537 res_clustering,
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
538 file = opt$HCPC_clust,
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
539 sep = "\t",
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
540 quote = F,
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
541 col.names = T,
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
542 row.names = F
8e17c31c536a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents: 3
diff changeset
543 )
5
569334568afa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
artbio
parents: 4
diff changeset
544 }